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The 49ers placed All-Pro outside linebacker Aldon Smith on the reserve/non-football injury list today, allowing him to seek treatment for what’s believed to be a substance-abuse problem

On Friday, Smith was arrested at 7:02 a.m. for suspicion of DUI, his second such charge in the past 20 months.

“Aldon Smith is taking a leave of absence to address a personal matter,” general manager Trent Baalke said. “The 49ers organization both respects and supports Aldon’s decision and commends him for taking responsibility for his actions. The long-term well-being of our players is paramount and we will stand by Aldon as he works toward addressing this issue. Due to the private nature of the matter, we will have no further comment.”

Said Smith: “I am taking a leave of absence to address my health. I am sorry that I have affected my team, my family and the organization. I will do everything in my power to handle this situation the best way possible. I appreciate the support of the 49ers and our fans.”

There is not a minimum amount of time Smith must remain on the NFI list. He can return to the team when he’s ready. It is common for treatment programs to last about a month. If Smith follows that timeline, a possible return date would be after the 49ers’ game in London against Jacksonville on Oct. 27. San Francisco has a bye the following week before hosting the Panthers on Nov. 10.

The 49ers don’t have to pay Smith while he’s on the NFI list. Cornerback Eric Wright is being paid a reduced salary of $10,000 per week on the NFI list, according to former NFL agent Joel Corry, who writes for CBS Sports. Wright, who has a $715,001 base salary, will earn about $42,000 per week when he’s active.

Smith is seeking treatment after a series of off-the-field incidents. In June 2012, he was stabbed in the early morning hours at a party at his house outside San Jose. He has been sued for unspecified damages by two Bay Area men who were shot at the party. One of the plaintiffs sued both Smith and his former teammate, Titans tight end Delanie Walker.

“I pray for him because he’s a good kid,” Walker said to the Tennessee media Monday. “He’s just making some bad choices now.”

The 49ers received an avalanche of media criticism for allowing Smith to play in Sunday’s 27-7 loss to the Colts given the circumstances. He was two days removed from his arrest and a day away from leaving the team to seek treatment. In defending the decision Sunday, CEO Jed York said he realized some wouldn’t agree with the team’s stance.

On Monday, Harbaugh was asked if he had any regrets about allowing Smith to play.

“Not going to rehash the decision,” he said. “We went over it last night. We did what we thought was in the best interest of the team and the best interest of the player long-term.”

In Smith’s absence, Dan Skuta and rookie Corey Lemonier will assume his role. It’s expected that Skuta will play in San Francisco’s base defense and Lemonier will take the field in pass-rushing situations. The 49ers can sign another player to fill Smith’s spot on the roster.